Workflow from Scientific Research

(Left) The preprocess of WGS data for downstream analysis. The WGS clean data were first aligned to rCRS. The mtDNA-mapped reads were then aligned to the reference containing nDNA and rCRS to remove the candidate ref-NUMTs covered by reads that were repetitively mapped to autosome and rCRS. The ref-NUMT free data were subsequently input to fNUMT for detecting non-ref NUTMs and NUMT-FPs. (Right) fNUMT searches the candidate junction reads with one end mapped to nDNA and the other to mtDNA. Then cluster such soft-clipped reads according to the mapping coordination and direction to locate the breakpoints of the inserted mtDNA segments and the insertion site on nDNA. Next, fNUMT assembly all the reads mapped to the candidate mtDNA segments and realign the contig to mtDNA to confirm the occurrence of the non-ref NUTMs and detect the mismatches that were the potential non-ref NUMT-FPs.

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